Twisted Pokemon
by Bowoneshi
Summary: Ash travels to Fuchsia City to find out that Koga is a member of Team Rocket. Then Cell comes from the future to absorb Mew and Mewtwo to achieve his complete form. Contains characters from several anime worlds. REWRITE OF MY DEBUT FANFIC!
1. Not Feeling Well? Must've Been the Fish

**Twisted Pokémon **

Chapter 1

**Not Feeling Well? Must've Been the Fish**

A young boy walks down a grass-lined road. The road was a small, dirt, country road. It probably didn't see many travelers. Behind him, a young girl was toting a small knapsack. Walking alongside her was a young man with an overly stuffed backpack with as many zippers and side compartments as there were blades of grass along the road. His nose was deep into the spine of a local traveler's guide. "We should reach the city gates within the hour," he quipped without removing his face from the guide. The boy grew a rather large smile and put some extra pep in his step. Riding his shoulders was a little Pikachu. Pikachu was a yellow electric Pokémon. When it stood upright it was about a foot tall. The chubby mouse had pointy black-tipped ears and a lightning bolt-shaped tail. It often sat on the boy's blue and white jacket. On top of his head was a red and white ball cap. Blue jeans, a green T-shirt, and white sneakers gave him a typical teenage look. His green, fingerless gloves rounded out his colorful outfit.

The girl stepped up to where the boy was walking to remind him, "Don't forget to rest at the Pokémon Center first."

"Of course, Misty, where else would I go?" said the boy, giving Misty a funny look.

"I know you all too well," Misty teased. "You'll run straight to the gym with worn-out Pokémon."

These three had traveled together for a long time. Misty was a tall red-haired teen with a low-cut pair of blue jean shorts and a yellow tank top with red suspenders. Her red hair was up in a ponytail on the left side of her head. She was a gym leader in the city of Cerulean with her sisters. Her specialty was water-type Pokémon. The youth of Kanto sometimes set out to become Pokémon masters. This journey would lead them all over the region, capturing and training Pokémon. To be the best, they had to win at gyms. Most towns had a gym. Every gym had a leader. If a trainer could beat the leader, they were awarded a badge as proof of their victory. If a trainer managed to beat all eight gyms, they could challenge the Pokémon league. The league is the king of all Pokémon challenges. Only the best of the best make it that far. And only the cream of the crop make it out victorious. The boy had won himself five badges. His sixth badge awaited him in the next town, Fuchsia City. The man was also a gym leader, a rock-type trainer from Pewter City.

Slowly over the horizon the Fuchsia City gates appeared. The boy's grin grew even bigger, and he started walking faster with each step, until he was in a full-on run. Misty rolled her eyes. "Ash, wait up," she whined, as she was forced to run in order to keep up with him. The man, also reluctant to run, walked behind a few more paces before launching himself into a run.

Ash stopped as he reached the gates. He slowly walked through in total amazement of the quiet little mountain city. In awe, he took in the beauty that surrounded him. His companions quickly caught up and stopped to gaze at the cityscape with Ash.

"Isn't it beautiful, Brock?" Ash asked the oldest member of the trio. Brock had quite the natural tan to match his dark, spiky hair. He wore a green T-shirt tucked under a brown vest. Green pants and black shoes made him look like quite the hiker.

"Yes, I've always wanted to visit the Safari Zone," he said. The Safari Zone was a one-of-a-kind national park. Here, for a small fee, one could explore the mountain forestry, and get an opportunity to catch extremely rare Pokémon. The Safari Zone was on the left of the band of travelers. To their right was the Pokémon Center and gym, nestled into the mountainside. They stood in the valley between which the city was set in. Down the main thoroughfare was lined with various shops and snack stands. "In fact, I think I'll take a look now," Brock added as the began walking in its direction.

Misty followed. "I heard there are some nice shops near there, too."

"How about we all meet back at the Pokémon Center in an hour," Brock suggested. Misty nodded; Ash didn't respond. As each traveled their own way, Ash was left standing at the gate, still staring at the city.

Pikachu poked his cheek. "Pika?" the Pokémon asked.

"Hmm, you're right, Pikachu. I'm hungry, too," Ash said as he started down the street, looking for a tasty stand.

"Get your tasty Magikarp Fish Sandwich here," shouted a man frying fish at his little stand. The man had purple hair, a red shirt, and a pair of blue jeans. Over top he wore an apron with the stand's logo on it.

"Or some fresh Goldeen Sticks," shouted a woman at the register. She was about the same age as the man. She had long red hair pulled back into a ponytail. She had the same red shirt and logo-imprinted apron.

"All for low, low prices," said a talking Meowth. Meowth typically didn't talk. They were a tan cat Pokémon with a gold coin on its head.

"Looks like fish is all that's on the menu," Ash said to Pikachu.

"Oh, we also have fried Doduo legs," the man interjected.

"We'll take two," Ash informed the man. He happily dropped a couple of legs into the deep fryer.

"That'll be ¥217," The woman told Ash.

"It'll take a couple of minutes," the man shouted over the sizzle of the deep fryer. "We have plenty of seating over there," he continued, pointing to a couple of patio tables to the left of the stand.

"We'll let you know when it's ready," said the Meowth. Pikachu jumped off onto the counter as Ash reached behind him to get some money. He paid the woman who smiled at him when he turned to go to the tables. He made it a few steps before he heard a loud thud. He glanced back to see Pikachu in a glass dome. The man and the woman tore off their mundane clothing to reveal Team Rocket uniforms.

Team Rocket was an evil organization that stole Pokémon for their own gain. These two have been after Ash's Pikachu since day one.

"Prepare for trouble," the woman said, striking a pose.

"Give me back my Pikachu!" Ash shouted, one hand pointing at them, the other clutched on one of many Pokéballs lining his belt.

"You should learn to respect your elders," the woman snapped.

"Sure thing, old lady," Ash smirked. A horrified expression overcame the woman.

"How dare you!" she snarled, reaching for her own Pokéball.

"Jesse, can I say my lines?" the man asked, disappointed he couldn't finish the infamous Team Rocket motto.

Jesse ignored the man's question and instead shouted, "Grab Pikachu and get outta here. I'll hold off the twerp."

The man grabbed Pikachu and ran to a hot air balloon hidden behind the stand. The balloon was a Meowth head tied to a small woven basket large enough for the two of them. Meowth followed the man. Even though it was a Pokémon, the chatting feline didn't do much fighting. The man gave Jesse a Pokéball before darting behind their makeshift business.

Jesse threw the man's Pokéball. "Go, Weezing," she called. The Pokéball landed in between her and Ash. The ball broke open and a flash of light filled the space between them. When the light faded, above where the Pokéball landed, a huge purple cloud floated there. It had two heads and was covered in pores. From these pores came poison gas.

Ash threw his Pokéball. After another flash of light, there stood a tiny blue turtle. "Squirtle, I choose you! Use water gun to free Pikachu," he commanded. The man was still trying to get the balloon off the ground.

"Not so fast," said Jesse. "Your battle is with me. Weezing, Smog now." A thick haze came from Weezing's pores.

"Squirtle!" Ash yelled. He couldn't see where his Pokémon was.

"Weezing, Tackle," Ash heard from across the haze. His Squirtle let out a cry of pain.

Ash threw another Pokéball into the dense smog. Out from this one came a large bird. "Pidgeotto, use Gust to get rid of this smog." The bird vigorously flapped its wings, and all the smog blew away. The current was also strong enough to send James, Meowth, and Pikachu high into the late afternoon sky. Ash ran past Jesse, his arm outstretched to the balloon sailing away with his Pokémon.

Jesse grabbed his shoulder. "The battle isn't over yet, twerp," she sneered.

Ash jerked his shoulder from her grip. "James will be back for you, won't he?"

Jesse raised an eyebrow. "I wouldn't advise scheming anything dangerous," she warned. "It's the quickest way to get burned." She threw a second Pokéball. From it came a giant purple snake. "Arbok, eat that turtle whole!"

The stage was set. A two-on-two Pokémon battle royale. Weezing and Arbok vs. Squirtle and Pidgeotto. "Pidgeotto, use Wing Attack on Arbok," Ash commanded. As the poison snake, mouth wide open, lunged at Squirtle, Pidgeotto stepped in the middle. Its wing were outstretched. Arbok smacked into it just below its chin. Arbok had just been clotheslined! It fell over backwards, gasping for air.

"Arbok, get up!" Jesse shouted. "Tch. Worthless. Weezing, Tackle!" she barked. The poison cloud slammed into Pidgeotto. The bird fell over but quickly regained posture. By this time, Arbok had gotten back up as well.

"Squirtle, Withdraw," Ash commanded. "Pidgeotto, take Squirtle up high." The turtle retreated into its shell. Pidgeotto picked Squirtle up with its claws, and soared up toward the setting sun.

Jesse grinned. "Trying to outsmart Team Rocket, are you? Well, it won't work."

"Watch me," Ash told her. "Pidgeotto, use Aerial Ace!" The bird Pokémon soared down at an incredibly fast speed, Squirtle still in tow. Pidgeotto smacked Weezing, beak first. The poison cloud fainted. "Now, drop Squirtle," Ash continued issuing commands. Pidgeotto did as it was told, dropping Squirtle right on Arbok's head. "Now, Squirtle, use Hydro Pump!" The tiny turtle popped out of its shell and hit Arbok at point blank range with a powerful stream of water. Arbok was knocked out, too. Ash had won the battle.

"Where's my Pikachu?" Ash asked.

"Maybe you should try the gym," Jesse suggested. "I hear it has ties to Team Rocket."

"Why don't you lead the way?" Ash added.

"Sorry, but I'm done with twerps like you," she said, and with that she ran into the crowd nearby.

"Wait!" Ash screamed, but it was too late.

…

Ash walked into the Pokémon Center. Brock and Misty were already at a booth waiting for him.

Misty jumped up from the table. "You'll never guess what I found," she said. Without giving him a chance to reply, she continued, "I got this uber-cute Jigglypuff purse. Oh, and these Seel slippers were 25% off!"

Ash just walked past her.

"Hey, where's Pikachu?" Misty asked, just realizing the small mouse was missing.

Ash didn't answer. He just sat down opposite Brock, and pulled down his hat over his eyes.

"What happened?" Brock asked, concerned about his friend and Pikachu.

"Team Rocket finally got Pikachu," Ash muttered under a stream of tears.

"Where did they go?" Misty asked, resuming her seat next to Brock.

"They said something about the gym." It was hard to understand him as he began to cry harder. The tears flooding the table in front of him. The small puddle grew more surface area with each drop. Gym was all Brock and Misty needed to hear.

Brock reached his arm across the table to console his friend. "It's getting late, but, first thing in the morning, we'll check out the gym and find out what's going on."

"Yea, we'll get Pikachu back, but first we need to rest," Misty agreed. "C'mon, we already rented us rooms for the night."

Ash and company headed to bed, but none of them would sleep.

**AN: After over four years, I'm back rewriting my debut fanfic, Twisted Pokémon. I hope you'll enjoy it. 'Til next time, chow!**

**~Bow.**


	2. A Warning Against Food Poisoning

**Twisted Pokémon**

Chapter 2

**A Warning Against Food Poisoning**

A man in a black suede suit sat behind a desk. The desk was in a dark room. The only light source was from a window behind the man. The curtains were closed, only allowing a few sparse rays of light to glimmer through. He leaned back in his big leather office chair. The man was a well-built, tall, middle-aged man. On his lap was a cat Pokémon. The cat was rather large and tan. It was a Persian, the evolved form of Meowth. It would purr when he pet it. Aside from the polished, wooden desk and leather chair, there was no other furniture in the room. There wasn't so much as a clock on the wall or a light from the ceiling. Opposite the window was a small door. A knock came from the other side. "Come in," The man said roughly. The door slowly opened. It was Jesse and James. Meowth came in behind them, carrying the glass dome with Pikachu still inside.

"Sir, we uh... we got Pikachu, sir," Jesse mumbled.

"About time," the man shouted. He shifted in his seat. "What the hell took so long?"

"We're sorry, sir," James apologized. "Some things came up, and..."

"Enough!" the man interrupted. "You've been chasing it for what? A year now? Two? And what do I want with it anyway?"

"It's a, um, quite powerful..." Jesse began.

"Power? I don't need power. I have the most powerful Pokémon in existence!"

"But, sir," James pleaded.

"All I want to know is if its worth anything." the man asked.

"I... I don't know, sir," Jesse stumbled around for an answer.

"I need to know," the man hollered. "Now go; quit wasting my time." He waved them out the door. The trio scurried away quickly.

Once they were away from the man's ears, James questioned Meowth, "I thought you said we would get promotions."

"Give him time," Meowth brushed off. "The boss will come around, you'll see. Then we'll all get big, fat raises!"

"I hope so," Jesse said doubtfully. "Wonder what Pokémon the boss has better than that twerp's Pikachu," she thought aloud.

"Who knows," shrugged the cat. "He probably has every Pokémon ever discovered."

"And maybe a few undiscovered ones, too," James added.

No one knew how true that statement was.

…

Ash, Misty, and Brock lay in bed. The sun was rising, filling their rooms with light. Not one of them slept that night. All three just laid there, staring at the ceiling as if they could see beyond it. Brock was first to break his fixation. He changed out of his pajamas and into his usual attire. He walked down the hall, knocking on Misty's and Ash's doors. The knocking pulled Misty from the land of the ceiling back down to Earth, but Ash's mind seemed out of reach, lost to the endless depths of the Pokémon Center ceiling.

Misty changed and joined Brock in front of Ash's room.

"Ash? You awake?" Brock asked, knocking once more.

"Ash, we're going to the gym today, remember? We'll get Pikachu back, I promise," Misty was talking to a lifeless door.

"We won't find Pikachu in there," Brock commented.

After waiting a few more seconds, Misty warned Ash, "Hope your decent, 'cause we're coming in." She opened the door, and her and Brock went inside. Ash was still in bed, eyes glued to the ceiling. He didn't even blink. "Ash." Misty sat next to him on his bed. "We need to do this. Don't you want Pikachu back?"

The rhetorical question snapped Ash out of his trance. His face became contorted with anger. Misty and Brock left so he could change. After he left his room, the three of them went downstairs for breakfast. No one spoke during the meal. Brock and Misty slowly ate their scrambled Pokémon eggs and Spoink bacon. Ash just used his fork to move and poke at his meal. After about twenty minutes, he just pushed the plate away and stared out the window until his friends had finished.

"You haven't even touched your plate," Misty noticed, breaking the long chain of silence. "Aren't you hungry?" Ash just shrugged his shoulders without looking away from the window.

"You'll need your strength today," Brock said.

"We're so close," Ash muttered. Misty and Brock looked at each other, confused. Ash continued, "Yet I've never felt so far away." Just next door, directly out the window Ash was gazing out of, was the Fuchsia City Pokémon Gym. Inside was his Pikachu and a deep secret. One that would determine the fate of Team Rocket. And the world.

Over their travels, Ash and Pikachu have become inseparable. This was heart wrenching for them both. Even though Ash and Pikachu were only feet apart, it felt like light years.

…

A young boy, about the same age as Ash, walked in through the front doors of the Fuchsia City Pokémon Gym. He challenged its leader, Koga, to a Pokémon battle, and won by a landslide. The boy received his badge and left.

Then the man in the suit from the dark room came out. "You are pathetic," the man told Koga. "What has gotten into you? You've lost every match since... since you left Team Rocket!"

"You know I don't want to do this," Koga replied. "I don't agree with what you've done."

"What I've done?" the man questioned. "It's what _you've_ done, Koga. Only you are to blame."

"That... that thing is your creation!" Koga retorted.

"I do believe you engineered him," the man corrected.

"I tried to quit when you went too far."

"And I told you what would happen if you did."

"Leave my daughter out of this!"

"Oh, Jasmine will be fine. _If_ you behave."

"And you know what will happen if you hurt me or my family."

"Yes, yes. I'm quite aware of your idle threats. I have connections. If your ninjas move, I'll know about it, and will be able to move accordingly."

"Then why am I still around? I've only become a liability."

"I think you are still of some use to me."

"Giovanni, you bastard! I'll never..."

"Oh, but Jasmine is just down the road."

"Touch her and you die!"

"Ha ha ha. Koga, you always keep me entertained. But I think if you lose the next match, it is _you_ who will die." With that, Giovanni retreated into his dark office.

Koga clinched his fists and muttered under his breath, "I swear to God, one day he will pay!"

…

Misty and Brock finished breakfast and didn't waste any time gearing up. They reassured Ash that Pikachu was safe. The three of them left the Pokémon Center and headed down the road to the gym. Ash's face grew stern, and he flipped his hat around to the back.

When they reached the gym, there were stairs leading up to a big glass set of double doors. At the bottom, on both sides of the steps stood the Pokémon League statues. These were in front of all the Pokémon gyms all across Kanto. This was engraved:

Fuchsia City Pokémon Gym

Leader: Koga

Winning Trainers:

Lance

Professor Samuel Oak

Agatha

Bruno

Lorlei

And freshly engraved at the bottom was none other than:

Gary Oak

Gary was a neighbor to Ash back in his hometown, Pallet Town. They were about the same age. Both have grown into remarkable trainers. Gary is the grandson to the world renown Professor of Pokémon, the legendary Samuel Oak. It was Professor Oak who gave both Ash and Gary their first Pokémon and sent them off with his invention, the Pokédex, to fill it with data from every kind of Pokémon out there. Since that day, Gary and Ash have been rivals, seeing which will be first to complete their two goals - filling the Pokédex and becoming a champion at the Pokémon League. So far, Gary has been a step ahead of Ash the entire time. This was no exception. Gary had come and gone, leaving his mark on the local gym statue, reminding Ash that he was still behind.

The trio marched up the steps and barged right into the gym. Koga stood at the other end of the large stadium. Ash walked up to him and shouted, "Where's my Pikachu?"

"Huh?" Koga was caught off guard.

"Jesse told my this gym was tied to Team Rocket," Ash continued. "And my Pikachu is in here. I'm not leaving until I get it back!"

"If you beat me in a battle, I'll take you to the leader of Team Rocket."

"And if I lose?" Ash asked.

"Then you turn around, leave, and never come back."

"Deal," Ash grabbed a Pokéball. The judge took his spot at the sidelines. Judges were always at gym battles to ensure a fair fight. "A 4-on-4 Gym Match, Leader Koga vs. Challenger Ash!"

With Ash being down his best Pokémon, this could be his most challenging fight yet!

**AN: Chapter 2 is finished! In only 2 days! Special thank you to my beta, Yuki Battosai, for reading, editing, re-reading, and re-editing both chapters for me. Hope I don't annoy her too much. ;p Please R&R. Tell me if you love it or hate it. Constructive criticism is welcome! Thank you all for reading. 'Til next time, chow!**

**~Bow**


End file.
